Calibration bar when using LUTs

[abhamacher]

Hi Will,

is it actually possible to add a calibration bar to the image when using LUTs in OMERO.figure? I don't think I ever saw such a function in OMERO.figure, although it's quite essential from my point of view. Maybe I just have overseen it?

Thanks, Anna

[will-moore]

Hi Anna, Can you add a screenshot to show what you're thinking of and how it's calibrated?

I'm trying to think how to achieve this by creating a "fake" file (https://docs.openmicroscopy.org/bio-formats/6.11.0/developers/generating-test-images.html) which normally are created with a grey-scale that you could then render with a chosen LUT.

I could imagine adding a calibration bar for an image to match it's current rendering settings, but then you'd need to update it if you changed the image's rendering settings...

[abhamacher]

Hi Will,

sorry, if I was not precise enough in my first post. With "calibration bar" I'm referring to the correspondent function in Fiji:

I can image this adds some complexity to OMERO.figure, but when using LUTs this is actually essential from my point of view.

[will-moore]

Ah, OK I see - thanks for the screenshot.

That would be a nice feature for OMERO.figure. I'll add it to the TODO list.

In the meantime, I played about a bit to see what you can do with existing functionality...

$ touch "calibration&sizeX=256&sizeY=256.fake"
$ omero import "calibration&sizeX=256&sizeY=256.fake"

...
Image:250772
Other imported objects:
Fileset:132614
...

Then "Add Image" in OMERO.figure, with this Image ID. I did this a couple of times for the screenshot. Then apply the LUT you want and resize / rotate (e.g. 270' for the vertical one) and add a couple of labels to the top and bottom (the labels in the horizontal ones are actually labels on the image panel bottom-left and bottom-right).

I realise that this isn't as nice as in Fiji, and it will give you an 'orphaned' calibration image which you could organise in a Dataset and use it for multiple figures. The lack of labels is an issue, but hopefully its partially useful?